recount3: summaries and queries for large-scale RNA-seq expression and splicing.

We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to the data, we provide the recount3 and snapcount R/Bioconductor packages as well as complementary web resources. Using these tools, data can be downloaded as study-level summaries or queried for specific exon-exon junctions, genes, samples, or other features.

Reference flow: reducing reference bias using multiple population genomes.

Most sequencing data analyses start by aligning sequencing reads to a linear reference genome, but failure to account for genetic variation leads to reference bias and confounding of results downstream. Other approaches replace the linear reference with structures like graphs that can include genetic variation, incurring major computational overhead. We propose the reference flow alignment method that uses multiple population reference genomes to improve alignment accuracy and reduce reference bias.

Osteomyelitis as a Result of Pancreaticojejunostomy Stent Migration after Whipple Procedure.

Pancreaticoduodenectomy, or Whipple procedure, is a high-risk surgical procedure commonly performed for tumors of the pancreatic head. The pancreatico-enteric anastomosis is an important component of this procedure. The maturation and adequate healing of this anastomotic site is critical to decrease the risk of postoperative pancreatic fistulas.

Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees.

Enormous databases of short-read RNA-seq experiments such as the NIH Sequencing Read Archive are now available. These databases could answer many questions about condition-specific expression or population variation, and this resource is only going to grow over time. However, these collections remain difficult to use due to the inability to search for a particular expressed sequence.

Fast search of thousands of short-read sequencing experiments.

The amount of sequence information in public repositories is growing at a rapid rate. Although these data are likely to contain clinically important information that has not yet been uncovered, our ability to effectively mine these repositories is limited. Here we introduce Sequence Bloom Trees (SBTs), a method for querying thousands of short-read sequencing experiments by sequence, 162 times faster than existing approaches.